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benkirk/sam-queries

https://github.com/benkirk/sam-queries · scanned 2026-06-17 01:39 UTC (1 month, 2 weeks ago)

203 raw signals (0 security + 203 graph)

UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 1 month, 2 weeks ago · v2 · last Δ -16.7 (diff) · 138 actionable findings from 1 signal source. 65 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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Corpus Intelligence Cross-corpus context (cohort percentile, top patterns, fix plan) is shown only on repositories you own. Sign up and connect your repo to view it.
Scan summary Repository scanned at 60.0/100 with 88.9% coverage. It contains 6275 nodes across 30 cross-layer flows, written primarily in mixed languages. Engine surfaced 203 findings — concentrated in quality (104), cicd (48), software (24). Risk profile is high: 3 critical, 16 high, 37 medium. Recommended next step: open the quality layer findings first — that's where the highest-impact wins live.

Showing 78 of 138 actionable findings. 203 raw detector signals were grouped into reader-sized issues. Click TP / FP to vote on a finding's accuracy — votes adjust the confidence weighting and improve detection across the platform.

critical System graph security Secrets conf 1.00 2 occurrences Possible secret in helm/local-secrets.sh
Detected pattern matching password_literal. Rotate the credential and move to a secret manager.
lines 26, 33
helm/local-secrets.sh:26, 33 (2 hits)
critical System graph security Secrets conf 1.00 Possible secret in infrastructure/README.md
Detected pattern matching password_literal. Rotate the credential and move to a secret manager.
infrastructure/README.md:60
high System graph security Agent instructions conf 1.00 Agent instruction/config may expose a secret: CLAUDE.md
Agent-facing files are routinely pasted into LLM/tool contexts. Move literal tokens, keys, and passwords into a secret manager or document them as placeholders only.
CLAUDE.md:694 SecretsClaude instruction
high System graph security auth conf 1.00 Flask mutation route `<anonymous>` without `@login_required` — src/webapp/auth/blueprint.py:53
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/auth/blueprint.py:53 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `ingest_casper` without `@login_required` — src/webapp/api/v1/status.py:248
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/status.py:248 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `ingest_derecho` without `@login_required` — src/webapp/api/v1/status.py:214
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/status.py:214 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `ingest_jupyterhub` without `@login_required` — src/webapp/api/v1/status.py:283
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/status.py:283 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `refresh_cache` without `@login_required` — src/webapp/api/v1/directory_access.py:82
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/directory_access.py:82 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `refresh_cache` without `@login_required` — src/webapp/api/v1/fstree_access.py:225
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/fstree_access.py:225 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `refresh_cache` without `@login_required` — src/webapp/api/v1/project_access.py:89
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/project_access.py:89 securityAuth flask unauth route
high System graph security auth conf 1.00 Flask mutation route `report_outage` without `@login_required` — src/webapp/api/v1/status.py:327
Flask route declares POST/PUT/DELETE/PATCH methods without an auth decorator. Add `@login_required` (Flask-Login) or equivalent.
src/webapp/api/v1/status.py:327 securityAuth flask unauth route
high System graph cicd CI/CD security conf 1.00 GitHub Action tracks a moving branch
trufflesecurity/trufflehog@main can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
.github/workflows/deploy-staging.yaml:38 CI/CD securitySupply chainGithub actions
high System graph cicd CI/CD security conf 1.00 GitHub Action tracks a moving branch
trufflesecurity/trufflehog@main can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
.github/workflows/ci-staging.yaml:34 CI/CD securitySupply chainGithub actions
high System graph security security conf 1.00 Insecure pattern 'subprocess_shell_true' in collectors/jupyterhub/collector.py:175
Found a known-risky pattern (subprocess_shell_true). Review and replace if possible.
collectors/jupyterhub/collector.py:175 Subprocess shell true
high System graph security security conf 1.00 Insecure pattern 'subprocess_shell_true' in collectors/lib/pbs_client.py:45
Found a known-risky pattern (subprocess_shell_true). Review and replace if possible.
collectors/lib/pbs_client.py:45 Subprocess shell true
high System graph security security conf 1.00 Insecure pattern 'subprocess_shell_true' in collectors/lib/ssh_utils.py:121
Found a known-risky pattern (subprocess_shell_true). Review and replace if possible.
collectors/lib/ssh_utils.py:121 Subprocess shell true
high System graph security security conf 1.00 Insecure pattern 'subprocess_shell_true' in containers/sam-sql-dev/bootstrap_clone.py:103
Found a known-risky pattern (subprocess_shell_true). Review and replace if possible.
containers/sam-sql-dev/bootstrap_clone.py:103 Subprocess shell true
high System graph security security conf 1.00 Insecure pattern 'tls_verify_false' in collectors/jupyterhub/collector.py:289
Found a known-risky pattern (tls_verify_false). Review and replace if possible.
collectors/jupyterhub/collector.py:289 Tls verify false
medium System graph quality Integrity conf 1.00 `fetch()` without try/.catch or AbortSignal — src/webapp/static/js/lazy-loading.js:14
Bare `fetch(...)` will throw an unhandled rejection on network failure. Wrap in try/catch, attach a `.catch(...)`, or pass an AbortSignal with a timeout.
runtime safetyRobustness
medium System graph quality Integrity conf 1.00 `fetch()` without try/.catch or AbortSignal — src/webapp/static/js/nav-view-persistence.js:84
Bare `fetch(...)` will throw an unhandled rejection on network failure. Wrap in try/catch, attach a `.catch(...)`, or pass an AbortSignal with a timeout.
runtime safetyRobustness
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: CLAUDE.md
This agent instruction grants code or shell authority but does not state the verification gate that decides promotion. The recurring safe pattern is: LLM proposes; deterministic tests/build/security checks verify; only verified code promotes.
CLAUDE.md VerificationClaude instruction
medium System graph quality Agent instructions conf 1.00 Agent authority lacks a verifier contract: docs/presentations/CLAUDE.md
This agent instruction grants code or shell authority but does not state the verification gate that decides promotion. The recurring safe pattern is: LLM proposes; deterministic tests/build/security checks verify; only verified code promotes.
docs/presentations/CLAUDE.md VerificationClaude instruction
medium System graph quality Placeholder conf 1.00 Critical user flow still appears backed by mock or placeholder data
A payment/auth/admin/order/billing-style flow contains mock, fake, TODO, dummy, or placeholder markers in runtime source. In the Fable corpus this is a high-leverage completeness smell: the app can look finished while the money, identity, or tenant flow is still scaffolded.
Mock dataCritical flowGenerated repo pattern
medium System graph hardware Security conf 1.00 Dockerfile runs as root: containers/collectors/Dockerfile
No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image.
Container
medium System graph hardware Security conf 1.00 Dockerfile runs as root: containers/sam-sql-dev/Dockerfile
No non-root USER set. Containers running as root expand the blast radius of any vulnerability inside the image.
Container
medium System graph cicd CI/CD security conf 1.00 20 occurrences GitHub Action is tag-pinned rather than SHA-pinned
docker/setup-qemu-action@v3 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
7 files, 20 locations
.github/workflows/build-images-cirrus-deploy.yaml:138, 141, 144, 152, 175 (5 hits)
.github/workflows/deploy-staging.yaml:30, 54, 62, 93, 100 (5 hits)
.github/workflows/ci-staging.yaml:57, 90, 113, 150 (4 hits)
.github/workflows/mega-linter.yaml:74, 113, 175 (3 hits)
.github/workflows/sam-ci-conda_make.yaml:71
.github/workflows/sam-ci-docker.yaml:43
.github/workflows/test-install.yaml:39
CI/CD securitySupply chainGithub actions
medium System graph cicd CI/CD security conf 1.00 4 occurrences GitHub Actions workflow grants broad write permissions
CI tokens with write permissions increase blast radius when an action, dependency, or PR workflow is compromised. Prefer job-level least-privilege permissions.
4 files, 4 locations
.github/workflows/build-images-cirrus-deploy.yaml
.github/workflows/clean-ghcr.yaml
.github/workflows/mega-linter.yaml
.github/workflows/sync-staging-to-main.yaml
CI/CD securitySupply chainGithub actions
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in src/webapp/static/js/fk-picker.js:74
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
src/webapp/static/js/fk-picker.js:74 Direct innerhtml assignment
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in src/webapp/static/js/form-helpers.js:25
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
src/webapp/static/js/form-helpers.js:25 Direct innerhtml assignment
medium System graph security security conf 1.00 Insecure pattern 'direct_innerhtml_assignment' in src/webapp/static/js/htmx-config.js:208
Found a known-risky pattern (direct_innerhtml_assignment). Review and replace if possible.
src/webapp/static/js/htmx-config.js:208 Direct innerhtml assignment
medium System graph quality Integrity conf 1.00 Network/subprocess call without timeout or try/except — containers/sam-sql-dev/bootstrap_clone.py:106
`subprocess.run(...)` here lacks both a `timeout=` arg and an enclosing try/except. This is exactly the class of bug that took down our git-clone earlier (HTTP/2 stream cancel surfaced as a fatal). Add a `timeout=` and wrap in try/except, or use a wrapper that retries.
runtime safetyRobustness
medium System graph quality Placeholder conf 1.00 Placeholder or mock-heavy implementation detected
Found 66 placeholder/mock markers across 17 source files. This often means the repo looks complete while core flows still use generated scaffolding or fake data.
Mock dataIncompleteGenerated repo pattern
medium System graph network Security conf 1.00 Privileged port 15 in use
Port 15 is privileged (<1024). Make sure the service runs with the right caps or front it with a non-privileged port via a load balancer.
.github/workflows/clean-ghcr.yaml Ports
low System graph quality Integrity conf 1.00 74 env vars used in code but missing from .env.example
Drift between code and config docs. The first few: `ALEMBIC_SYSTEM_STATUS_URL`, `ALLOCATION_USAGE_CACHE_SIZE`, `ALLOCATION_USAGE_CACHE_TTL`, `API_TIMEOUT`, `AUDIT_ENABLED`, `AUDIT_LOG_PATH`, `AUTH_PROVIDER`, `BUILD_DATE` + 66 more. Add them (with a placeholder/comment) to .env.example so onboarding…
config drift
low System graph quality Debug conf 1.00 Debug logging residue appears in source files
Found 700 console/debugger/print-style debug statements in non-test source. This is a common fast-generation residue before production cleanup.
CleanupRepo hardeningGenerated repo pattern
low System graph hardware Supply chain conf 1.00 Docker base image is tag-pinned but not digest-pinned: mysql:9
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
containers/sam-sql-dev/Dockerfile:1 containersPinned dependencies
low System graph hardware Supply chain conf 1.00 Docker base image is tag-pinned but not digest-pinned: python:3
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
containers/webapp/Dockerfile:1 containersPinned dependencies
low System graph hardware Supply chain conf 1.00 Docker base image is tag-pinned but not digest-pinned: python:3
Container tags can be retagged upstream. Pin production base images to a reviewed digest (`image@sha256:...`) when reproducibility and supply-chain integrity matter.
containers/collectors/Dockerfile:1 containersPinned dependencies
low System graph cicd CI/CD security conf 1.00 22 occurrences GitHub Action is tag-pinned rather than SHA-pinned
actions/checkout@v4 can move without a code change in this repo. Pin third-party actions to a reviewed 40-character commit SHA.
9 files, 22 locations
.github/workflows/build-images-cirrus-deploy.yaml:135, 230, 248, 253, 287, 293 (6 hits)
.github/workflows/ci-staging.yaml:29, 51, 64, 87, 110, 145 (6 hits)
.github/workflows/deploy-staging.yaml:25, 49 (2 hits)
.github/workflows/mega-linter.yaml:61, 101 (2 hits)
.github/workflows/sam-ci-docker.yaml:36, 165 (2 hits)
.github/workflows/clean-ghcr.yaml:18
.github/workflows/sam-ci-conda_make.yaml:53
.github/workflows/sync-staging-to-main.yaml:35
CI/CD securitySupply chainGithub actions
low System graph security security conf 1.00 Insecure pattern 'debug_true' in src/webapp/run.py:420
Found a known-risky pattern (debug_true). Review and replace if possible.
src/webapp/run.py:420 Debug true
low System graph quality Integrity conf 1.00 12 occurrences Near-duplicate function bodies in 2 places
Functions with the same first-5-line body hash: containers/sam-sql-dev/bootstrap_clone.py:dump_table_full, containers/sam-sql-dev/bootstrap_clone.py:dump_table_where This is *the* AI-coder failure mode (4× more duplication in vibe-coded repos — see https://jw.hn/ai-code-hygiene). Consolidate or do…
12 occurrences
repo-level (12 hits)
duplicatesduplication
low System graph quality Integrity conf 1.00 2 occurrences Near-duplicate function bodies in 3 places
Functions with the same first-5-line body hash: utils/profiling/profile_admin_orgs.py:before, utils/profiling/profile_user_dashboard.py:before, utils/profiling/profile_allocations.py:before This is *the* AI-coder failure mode (4× more duplication in vibe-coded repos — see https://jw.hn/ai-code-hyg…
2 occurrences
repo-level (2 hits)
duplicatesduplication
low System graph quality Integrity conf 1.00 4 occurrences Near-duplicate function bodies in 4 places
Functions with the same first-5-line body hash: src/webapp/utils/rbac.py:decorator, src/webapp/utils/rbac.py:decorator, src/webapp/utils/rbac.py:decorator, src/webapp/utils/rbac.py:decorator This is *the* AI-coder failure mode (4× more duplication in vibe-coded repos — see https://jw.hn/ai-code-hy…
4 occurrences
repo-level (4 hits)
duplicatesduplication
low System graph quality Integrity conf 1.00 Near-duplicate function bodies in 7 places
Functions with the same first-5-line body hash: src/webapp/api/access_control.py:decorator, src/webapp/api/access_control.py:decorator, src/webapp/api/access_control.py:decorator, src/webapp/api/access_control.py:decorator This is *the* AI-coder failure mode (4× more duplication in vibe-coded repo…
duplicatesduplication
low System graph quality Integrity conf 1.00 Near-duplicate function bodies in 8 places
Functions with the same first-5-line body hash: src/webapp/api/access_control.py:decorated_function, src/webapp/api/access_control.py:decorated_function, src/webapp/api/access_control.py:decorated_function, src/webapp/api/access_control.py:decorated_function This is *the* AI-coder failure mode (4×…
duplicatesduplication
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `child_old` in src/sam/manage/allocations.py:377
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `expected_legacy` in tests/unit/test_accounting_models.py:66
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `intended_old` in tests/unit/test_remediation_audit_trail.py:56
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `intended_old` in utils/remediation/fix_cesm0002_audit_trail.py:132
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `n_deleted_legacy` in src/cli/accounting/commands.py:751
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `test_replace_true_logs_delete_transaction_on_old` in tests/unit/test_renew_extend.py:877
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph quality Integrity conf 1.00 Old/deprecated-named symbol `user_old` in tests/unit/test_current_disk_usage.py:225
Names with suffixes like `_old`, `_v1`, `_deprecated` usually indicate replaced-but-not-removed code (typical AI-coder leftover). Confirm and delete, or rename if it's the active version.
old markerDead code
low System graph software Dead code conf 1.00 3 occurrences Possibly dead Python function: after
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
3 files, 3 locations
utils/profiling/profile_admin_orgs.py:61
utils/profiling/profile_allocations.py:100
utils/profiling/profile_user_dashboard.py:88
low System graph software Dead code conf 1.00 3 occurrences Possibly dead Python function: before
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
3 files, 3 locations
utils/profiling/profile_admin_orgs.py:58
utils/profiling/profile_allocations.py:97
utils/profiling/profile_user_dashboard.py:85
low System graph software Dead code conf 1.00 Possibly dead Python function: can_access_edit_project_page
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/utils/project_permissions.py:78
low System graph software Dead code conf 1.00 Possibly dead Python function: cleanup_temp_config_files
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
containers/sam-sql-dev/bootstrap_clone.py:70
low System graph software Dead code conf 1.00 3 occurrences Possibly dead Python function: decorator
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
3 files, 3 locations
src/webapp/api/access_control.py:398
src/webapp/utils/api_auth.py:131
src/webapp/utils/rbac.py:596
low System graph software Dead code conf 1.00 Possibly dead Python function: error_response
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/api/helpers.py:218
low System graph software Dead code conf 1.00 Possibly dead Python function: format_active_status
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/admin/custom_model_views.py:16
low System graph software Dead code conf 1.00 Possibly dead Python function: format_deleted_status
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/admin/custom_model_views.py:22
low System graph software Dead code conf 1.00 Possibly dead Python function: inaccessible_callback
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/admin/default_model_views.py:80
low System graph software Dead code conf 1.00 Possibly dead Python function: normalize_gecos
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
utils/parity/helpers.py:27
low System graph software Dead code conf 1.00 Possibly dead Python function: parse_input_start_date
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/api/helpers.py:45
low System graph software Dead code conf 1.00 Possibly dead Python function: post_fork
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
containers/webapp/gunicorn_config.py:27
low System graph software Dead code conf 1.00 Possibly dead Python function: require_any_permission
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/utils/rbac.py:562
low System graph software Dead code conf 1.00 Possibly dead Python function: require_permission_decorator
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/api/access_control.py:88
low System graph software Dead code conf 1.00 Possibly dead Python function: require_role
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/utils/rbac.py:585
low System graph software Dead code conf 1.00 Possibly dead Python function: success_response
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/api/helpers.py:197
low System graph software Dead code conf 1.00 Possibly dead Python function: topo_sort_all_tables
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
containers/sam-sql-dev/bootstrap_clone.py:243
low System graph software Dead code conf 1.00 Possibly dead Python function: vendor_assets_context_processor
No callers detected by AST scan in this repo. Could be exported for external callers or a framework handler.
src/webapp/vendor_assets.py:81
low System graph quality Complexity conf 1.00 Very large file: src/cli/accounting/commands.py (2009 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/sam/projects/projects.py (1566 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/sam/queries/allocations.py (1219 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/webapp/dashboards/admin/projects_routes.py (2475 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: src/webapp/dashboards/user/blueprint.py (1425 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: tests/unit/test_allocations_performance.py (1283 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: tests/unit/test_query_functions.py (1675 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
low System graph quality Complexity conf 1.00 Very large file: tests/unit/test_reconcile_quotas.py (1326 lines)
Files with >800 lines often hide complexity hotspots and discourage tests.
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